[BioC] problems installing VariantFiltering package

[Robert Castelo]

hi Daniel, i hope you don't mind i carbon copy the Bioconductor mailing 
list, as this problem you have may occur to other people who want to use 
VariantFiltering and in this way they'll find the answer if they google 
for this same question.

the problem you are reporting below comes from the fact that you are 
using Bioconductor 2.13 bound to R version 3.0.2 while VariantFiltering 
only entered the latest release of Bioconductor 2.14 which is bound to R 
version 3.1.0, and therefore, it does not exist in previous releases of 
Bioconductor.

you have to upgrade your installation of R to the latest one (3.1.0) and 
then install VariantFiltering.


best regards,

robert.

On 05/19/2014 04:19 PM, Daniel Benitez Rivera wrote:
> Dear Robert,
>
> I' m having problems installing VariantFiltering package. I don't
> understand much of the error, but I copy the R-console log here:
>
>>  install.packages("~/Escritorio/VariantFiltering_1.1.3.tar.gz", repos = NULL, type ="source")
> Installing package into ‘/home/daniel/R/x86_64-pc-linux-gnu-library/3.0’
> (as ‘lib’ is unspecified)
> ERROR: dependencies ‘S4Vectors’, ‘GenomeInfoDb’, ‘BSgenome.Hsapiens.UCSC.hg19’, ‘shiny’ are not available for package ‘VariantFiltering’
> * removing ‘/home/daniel/R/x86_64-pc-linux-gnu-library/3.0/VariantFiltering’
> Warning in install.packages :
>    installation of package ‘/home/daniel/Escritorio/VariantFiltering_1.1.3.tar.gz’ had non-zero exit status
>
>
> that's when I try to install it from source (a tar.gz file downloaded frombioconductor.org  <http://bioconductor.org>). When I try to install with
>
> source("http://bioconductor.org/biocLite.R")
>      biocLite("VariantFiltering")
>
>
> I got this:
>
>>  source("http://bioconductor.org/biocLite.R")
>
> Bioconductor version 2.13 (BiocInstaller 1.12.1), ?biocLite for help
> A newer version of Bioconductor is available after installing a new version of R,
>    ?BiocUpgrade for help
>>  biocLite("VariantFiltering")
> BioC_mirror:http://bioconductor.org
> Using Bioconductor version 2.13 (BiocInstaller 1.12.1), R version 3.0.2.
> Installing package(s)'VariantFiltering'
> Mensajes de aviso perdidos
> 1: package ‘VariantFiltering’ is not available (for R version 3.0.2)
> 2: installed directory not writable, cannot update packages'annotate',
>    'aroma.affymetrix','aroma.apd','aroma.core','BiocInstaller','caTools','gdata',
>    'gplots','gtools','IRanges','limma','matrixStats','optparse','PSCBS',
>    'R.devices','R.filesets','R.huge','R.methodsS3','R.oo','R.rsp','Rsamtools',
>    'rtracklayer','R.utils','truncnorm','xtable','boot','class','cluster',
>    'foreign','KernSmooth','lattice','MASS','Matrix','mgcv','nlme','nnet',
>    'rpart','spatial','survival'
>
>
> maybe the version of R or Bioconductor isn't right?
>
> thanks a lot!!!
>
>
> --
> *Daniel Benitez Rivera*
> /Asistente de Investigación/
> /Bioinformática/
> *Centro de Biotecnología*
> *Universidad de Concepción*
> Fono: (56)9-62207479

-- 
Robert Castelo, PhD
Associate Professor
Dept. of Experimental and Health Sciences
Universitat Pompeu Fabra (UPF)
Barcelona Biomedical Research Park (PRBB)
Dr Aiguader 88
E-08003 Barcelona, Spain
telf: +34.933.160.514
fax: +34.933.160.550